From ef7b8ab1a628c3fa8aefb3fd5da2ffc17afe8e53 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Thu, 9 Feb 2023 13:38:25 -0500
Subject: [PATCH 01/13] Created data-search, translating search.sh to JS

---
 src/data-search.js | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 src/data-search.js

diff --git a/src/data-search.js b/src/data-search.js
new file mode 100644
index 0000000..617c8b3
--- /dev/null
+++ b/src/data-search.js
@@ -0,0 +1,20 @@
+#! /usr/bin/env node
+
+// here we will convert the search.sh script into JS
+import { format, sub } from 'date-fns';
+import fs from 'fs';
+import { download, search } from './cli.js';
+
+const CATEGORY_ID = 'alzheimers-disease';
+const DATA_DIRECTORY = '../example-data';
+
+const MEDRXIV_SOURCE = 'medrxiv';
+const BIORXIV_SOURCE = 'biorxiv';
+
+const now = new Date();
+const startOffset = { months: 1 };
+const START_DATE = format(sub(now, startOffset), 'yyyy-MM-dd');
+const END_DATE = format(now, 'yyyy-MM-dd');
+
+const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
+const dataFile = fs.openSync(DATA_FILE, 'w');

From e69d2034e01fa1862b3eb6a8e3e2e3b1fb9d11fc Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Thu, 9 Feb 2023 14:38:46 -0500
Subject: [PATCH 02/13] added some minor changes

---
 src/data-search.js | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/data-search.js b/src/data-search.js
index 617c8b3..f5f4b01 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -16,5 +16,9 @@ const startOffset = { months: 1 };
 const START_DATE = format(sub(now, startOffset), 'yyyy-MM-dd');
 const END_DATE = format(now, 'yyyy-MM-dd');
 
+console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
+download(START_DATE, END_DATE, BIORXIV_SOURCE);
+
+console.log('Combining results...');
 const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
 const dataFile = fs.openSync(DATA_FILE, 'w');

From 3179ef126af2d379223ba297dbb7fbbf3d5e3f02 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Fri, 10 Feb 2023 16:06:35 -0500
Subject: [PATCH 03/13] environment / script improvements

---
 .vscode/launch.json | 10 ++++++++++
 scripts/date.js     |  2 +-
 src/data-search.js  | 17 +++++++++++++++--
 3 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/.vscode/launch.json b/.vscode/launch.json
index b39990a..6bd55bc 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -52,6 +52,16 @@
         "--pretty"
       ],
       "console": "integratedTerminal"
+    },
+    {
+      "type": "node",
+      "request": "launch",
+      "name": "DataSearch",
+      "skipFiles": [
+        "<node_internals>/**"
+      ],
+      "program": "${workspaceFolder}/src/data-search.js",
+      "console": "integratedTerminal"
     }
   ]
 }
\ No newline at end of file
diff --git a/scripts/date.js b/scripts/date.js
index cfba5c2..96fb7cd 100644
--- a/scripts/date.js
+++ b/scripts/date.js
@@ -1,6 +1,6 @@
 import { format, sub } from 'date-fns';
 
-const startOffset = { months: 1 };
+const startOffset = { days: 1 };
 const arg = process.argv[2];
 const now = new Date();
 
diff --git a/src/data-search.js b/src/data-search.js
index f5f4b01..7152dd6 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -3,6 +3,7 @@
 // here we will convert the search.sh script into JS
 import { format, sub } from 'date-fns';
 import fs from 'fs';
+import { options } from 'preact';
 import { download, search } from './cli.js';
 
 const CATEGORY_ID = 'alzheimers-disease';
@@ -17,8 +18,20 @@ const START_DATE = format(sub(now, startOffset), 'yyyy-MM-dd');
 const END_DATE = format(now, 'yyyy-MM-dd');
 
 console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-download(START_DATE, END_DATE, BIORXIV_SOURCE);
+download(START_DATE, END_DATE, BIORXIV_SOURCE); // not sure if the 3rd param is correct here
+// is just calling the download function enough? do we add something to account for the --output part in the script
+
+console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
+download(START_DATE, END_DATE, MEDRXIV_SOURCE); // not sure if the 3rd param is correct here
+// is just calling the download function enough? do we add something to account for the --output part in the script
 
 console.log('Combining results...');
 const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
-const dataFile = fs.openSync(DATA_FILE, 'w');
+const dataFile = fs.openSync(DATA_FILE, 'w'); // unsure about this solution as well to create a new file
+
+const QUERY = 'alzheimer';
+const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;
+console.log(`Searching for ${QUERY}`);
+const searchHits = search(QUERY, true); // also unsure about param 2
+const numSearchHits = Object.keys(searchHits).length;
+console.log(`Found ${numSearchHits} hits`);

From e9f4d1ff9735bc62982d4637a0a9cdb8e61d49c1 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Mon, 13 Feb 2023 18:00:15 -0500
Subject: [PATCH 04/13] edits to cli.js, allows debugging of data-search

---
 src/cli.js         |  6 +++---
 src/data-search.js | 34 +++++++++++++++++-----------------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/src/cli.js b/src/cli.js
index 89a5875..cbf1c58 100755
--- a/src/cli.js
+++ b/src/cli.js
@@ -17,7 +17,7 @@ const writeText = async (text, file) => await writeFile(file, text);
 const printText = text => console.log(text);
 const getPrettyText = (articles, queryString, options) => prettyArticles(articles, queryString, options);
 
-async function search (queryString, options) {
+export async function search (queryString, options) {
   const searcher = new Search();
 
   const articles = await getInput(options);
@@ -31,7 +31,7 @@ async function search (queryString, options) {
   await sendOutput(res, options, queryString);
 }
 
-async function download (startDate, endDate, options) {
+export async function download (startDate, endDate, options) {
   const source = options.source ?? 'biorxiv';
 
   const res = await performDownload(source, startDate, endDate);
@@ -103,4 +103,4 @@ async function main () {
   await program.parseAsync();
 }
 
-main();
+// main();
diff --git a/src/data-search.js b/src/data-search.js
index 7152dd6..870c5e1 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -2,9 +2,9 @@
 
 // here we will convert the search.sh script into JS
 import { format, sub } from 'date-fns';
-import fs from 'fs';
+// import fs from 'fs';
 import { options } from 'preact';
-import { download, search } from './cli.js';
+import { download } from './cli.js';
 
 const CATEGORY_ID = 'alzheimers-disease';
 const DATA_DIRECTORY = '../example-data';
@@ -13,25 +13,25 @@ const MEDRXIV_SOURCE = 'medrxiv';
 const BIORXIV_SOURCE = 'biorxiv';
 
 const now = new Date();
-const startOffset = { months: 1 };
+const startOffset = { days: 1 };
 const START_DATE = format(sub(now, startOffset), 'yyyy-MM-dd');
 const END_DATE = format(now, 'yyyy-MM-dd');
 
 console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
 download(START_DATE, END_DATE, BIORXIV_SOURCE); // not sure if the 3rd param is correct here
-// is just calling the download function enough? do we add something to account for the --output part in the script
+// // is just calling the download function enough? do we add something to account for the --output part in the script
 
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-download(START_DATE, END_DATE, MEDRXIV_SOURCE); // not sure if the 3rd param is correct here
-// is just calling the download function enough? do we add something to account for the --output part in the script
-
-console.log('Combining results...');
-const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
-const dataFile = fs.openSync(DATA_FILE, 'w'); // unsure about this solution as well to create a new file
-
-const QUERY = 'alzheimer';
-const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;
-console.log(`Searching for ${QUERY}`);
-const searchHits = search(QUERY, true); // also unsure about param 2
-const numSearchHits = Object.keys(searchHits).length;
-console.log(`Found ${numSearchHits} hits`);
+// download(START_DATE, END_DATE, MEDRXIV_SOURCE); // not sure if the 3rd param is correct here
+// // is just calling the download function enough? do we add something to account for the --output part in the script
+
+// console.log('Combining results...');
+// const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
+// const dataFile = fs.openSync(DATA_FILE, 'w'); // unsure about this solution as well to create a new file
+
+// const QUERY = 'alzheimer';
+// const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;
+// console.log(`Searching for ${QUERY}`);
+// const searchHits = search(QUERY, true); // also unsure about param 2
+// const numSearchHits = Object.keys(searchHits).length;
+// console.log(`Found ${numSearchHits} hits`);

From 0d821c902d5429b138bc142761b011d8b1a6349c Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Tue, 14 Feb 2023 18:12:15 -0500
Subject: [PATCH 05/13] Can create & write JSONs for both preprint sources

---
 src/data-search.js | 31 ++++++++++++++++++++++---------
 1 file changed, 22 insertions(+), 9 deletions(-)

diff --git a/src/data-search.js b/src/data-search.js
index 870c5e1..0563143 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -2,12 +2,11 @@
 
 // here we will convert the search.sh script into JS
 import { format, sub } from 'date-fns';
-// import fs from 'fs';
-import { options } from 'preact';
+import fs from 'fs';
 import { download } from './cli.js';
 
 const CATEGORY_ID = 'alzheimers-disease';
-const DATA_DIRECTORY = '../example-data';
+const DATA_DIRECTORY = 'example-data';
 
 const MEDRXIV_SOURCE = 'medrxiv';
 const BIORXIV_SOURCE = 'biorxiv';
@@ -17,17 +16,31 @@ const startOffset = { days: 1 };
 const START_DATE = format(sub(now, startOffset), 'yyyy-MM-dd');
 const END_DATE = format(now, 'yyyy-MM-dd');
 
+// Getting latest articles from BiorXiv
 console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-download(START_DATE, END_DATE, BIORXIV_SOURCE); // not sure if the 3rd param is correct here
-// // is just calling the download function enough? do we add something to account for the --output part in the script
-
+const options = {
+  source: 'biorxiv',
+  output: `${DATA_DIRECTORY}/${END_DATE}_${BIORXIV_SOURCE}.json`
+};
+fs.open(options.output, 'w', function (err, file) { // consider changing the callback function if needed
+  if (err) throw err;
+  console.log('Saved!');
+});
+download(START_DATE, END_DATE, options);
+
+// Getting latest articles from MedrXiv
+options.source = 'medrxiv';
+options.output = `${DATA_DIRECTORY}/${END_DATE}_${MEDRXIV_SOURCE}.json`;
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-// download(START_DATE, END_DATE, MEDRXIV_SOURCE); // not sure if the 3rd param is correct here
-// // is just calling the download function enough? do we add something to account for the --output part in the script
+fs.open(options.output, 'w', function (err, file) { // consider changing the callback function if needed
+  if (err) throw err;
+  console.log('Saved!');
+});
+download(START_DATE, END_DATE, options);
 
 // console.log('Combining results...');
 // const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
-// const dataFile = fs.openSync(DATA_FILE, 'w'); // unsure about this solution as well to create a new file
+// const dataFile = fs.openSync(DATA_FILE, 'w');
 
 // const QUERY = 'alzheimer';
 // const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;

From d16ebf5805d7d78fc6b2fc78927a16cdd0b2b055 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Wed, 15 Feb 2023 17:17:35 -0500
Subject: [PATCH 06/13] Both JSON files correctly populated

---
 src/data-search.js | 35 ++++++++++++++++++++---------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/src/data-search.js b/src/data-search.js
index 0563143..b1cfca2 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -16,29 +16,34 @@ const startOffset = { days: 1 };
 const START_DATE = format(sub(now, startOffset), 'yyyy-MM-dd');
 const END_DATE = format(now, 'yyyy-MM-dd');
 
+const BIORXIV_FILE = `${DATA_DIRECTORY}/${END_DATE}_${BIORXIV_SOURCE}.json`;
+const MEDRXIV_FILE = `${DATA_DIRECTORY}/${END_DATE}_${MEDRXIV_SOURCE}.json`;
+
+// Creating files for each data source
+fs.open(BIORXIV_FILE, 'w', function (err, file) { // consider changing the callback function if needed
+  if (err) throw err;
+  console.log('Saved!');
+});
+fs.open(MEDRXIV_FILE, 'w', function (err, file) { // consider changing the callback function if needed
+  if (err) throw err;
+  console.log('Saved!');
+});
+
 // Getting latest articles from BiorXiv
 console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
 const options = {
-  source: 'biorxiv',
-  output: `${DATA_DIRECTORY}/${END_DATE}_${BIORXIV_SOURCE}.json`
+  source: BIORXIV_SOURCE,
+  output: BIORXIV_FILE
 };
-fs.open(options.output, 'w', function (err, file) { // consider changing the callback function if needed
-  if (err) throw err;
-  console.log('Saved!');
-});
-download(START_DATE, END_DATE, options);
+await download(START_DATE, END_DATE, options);
 
 // Getting latest articles from MedrXiv
-options.source = 'medrxiv';
-options.output = `${DATA_DIRECTORY}/${END_DATE}_${MEDRXIV_SOURCE}.json`;
+options.source = MEDRXIV_SOURCE;
+options.output = MEDRXIV_FILE;
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-fs.open(options.output, 'w', function (err, file) { // consider changing the callback function if needed
-  if (err) throw err;
-  console.log('Saved!');
-});
-download(START_DATE, END_DATE, options);
+await download(START_DATE, END_DATE, options);
 
-// console.log('Combining results...');
+console.log('Combining results...');
 // const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
 // const dataFile = fs.openSync(DATA_FILE, 'w');
 

From 041935603d045e0ce6694ff74f26084d2c7b21fa Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Thu, 16 Feb 2023 14:15:42 -0500
Subject: [PATCH 07/13] Added different objects to correct download task

---
 src/data-search.js | 43 ++++++++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/src/data-search.js b/src/data-search.js
index b1cfca2..63b68f2 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -18,38 +18,47 @@ const END_DATE = format(now, 'yyyy-MM-dd');
 
 const BIORXIV_FILE = `${DATA_DIRECTORY}/${END_DATE}_${BIORXIV_SOURCE}.json`;
 const MEDRXIV_FILE = `${DATA_DIRECTORY}/${END_DATE}_${MEDRXIV_SOURCE}.json`;
+const COMBINED_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
+const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;
 
-// Creating files for each data source
+// Getting all latest articles from BiorXiv
+console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
 fs.open(BIORXIV_FILE, 'w', function (err, file) { // consider changing the callback function if needed
   if (err) throw err;
   console.log('Saved!');
 });
-fs.open(MEDRXIV_FILE, 'w', function (err, file) { // consider changing the callback function if needed
-  if (err) throw err;
-  console.log('Saved!');
-});
-
-// Getting latest articles from BiorXiv
-console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-const options = {
+const bioInfo = {
   source: BIORXIV_SOURCE,
   output: BIORXIV_FILE
 };
-await download(START_DATE, END_DATE, options);
+download(START_DATE, END_DATE, bioInfo);
 
-// Getting latest articles from MedrXiv
-options.source = MEDRXIV_SOURCE;
-options.output = MEDRXIV_FILE;
+// Getting all latest articles from MedrXiv
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-await download(START_DATE, END_DATE, options);
+fs.open(MEDRXIV_FILE, 'w', function (err, file) {
+  if (err) throw err;
+  console.log('Saved!');
+});
+const medInfo = {
+  source: MEDRXIV_SOURCE,
+  output: MEDRXIV_FILE
+};
+download(START_DATE, END_DATE, medInfo);
 
+// Creating a JSON with all the results, both sources combined
 console.log('Combining results...');
-// const DATA_FILE = `${DATA_DIRECTORY}/${END_DATE}.json`;
-// const dataFile = fs.openSync(DATA_FILE, 'w');
+fs.open(COMBINED_FILE, 'w', function (err, file) {
+  if (err) throw err;
+  console.log('Saved!');
+});
 
+// Search for the QUERY keyword in all the downloaded articles & compile the related articles
 // const QUERY = 'alzheimer';
-// const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;
 // console.log(`Searching for ${QUERY}`);
 // const searchHits = search(QUERY, true); // also unsure about param 2
 // const numSearchHits = Object.keys(searchHits).length;
 // console.log(`Found ${numSearchHits} hits`);
+fs.open(OUTPUT_FILE, 'w', function (err, file) {
+  if (err) throw err;
+  console.log('Saved!');
+});

From 8734bb121a26aba7d45992d36267a8b7d7443cc0 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Fri, 17 Feb 2023 19:48:38 -0500
Subject: [PATCH 08/13] Creating file output for combined results

---
 src/cli.js         |  2 +-
 src/data-search.js | 22 +++++++++++++++-------
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/src/cli.js b/src/cli.js
index cbf1c58..ae6d66c 100755
--- a/src/cli.js
+++ b/src/cli.js
@@ -39,7 +39,7 @@ export async function download (startDate, endDate, options) {
   await sendOutput(res, options);
 }
 
-async function sendOutput (res, options, queryString) {
+export async function sendOutput (res, options, queryString) {
   if (options.reverse) {
     res = res.reverse();
   }
diff --git a/src/data-search.js b/src/data-search.js
index 63b68f2..1652042 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -3,7 +3,7 @@
 // here we will convert the search.sh script into JS
 import { format, sub } from 'date-fns';
 import fs from 'fs';
-import { download } from './cli.js';
+import { download, sendOutput } from './cli.js';
 
 const CATEGORY_ID = 'alzheimers-disease';
 const DATA_DIRECTORY = 'example-data';
@@ -31,7 +31,7 @@ const bioInfo = {
   source: BIORXIV_SOURCE,
   output: BIORXIV_FILE
 };
-download(START_DATE, END_DATE, bioInfo);
+const bioData = await download(START_DATE, END_DATE, bioInfo);
 
 // Getting all latest articles from MedrXiv
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
@@ -43,7 +43,7 @@ const medInfo = {
   source: MEDRXIV_SOURCE,
   output: MEDRXIV_FILE
 };
-download(START_DATE, END_DATE, medInfo);
+const medData = await download(START_DATE, END_DATE, medInfo);
 
 // Creating a JSON with all the results, both sources combined
 console.log('Combining results...');
@@ -51,6 +51,14 @@ fs.open(COMBINED_FILE, 'w', function (err, file) {
   if (err) throw err;
   console.log('Saved!');
 });
+const combinedData = {
+  ...bioData,
+  ...medData
+};
+const combinedInfo = {
+  output: COMBINED_FILE
+};
+sendOutput(combinedData, combinedInfo);
 
 // Search for the QUERY keyword in all the downloaded articles & compile the related articles
 // const QUERY = 'alzheimer';
@@ -58,7 +66,7 @@ fs.open(COMBINED_FILE, 'w', function (err, file) {
 // const searchHits = search(QUERY, true); // also unsure about param 2
 // const numSearchHits = Object.keys(searchHits).length;
 // console.log(`Found ${numSearchHits} hits`);
-fs.open(OUTPUT_FILE, 'w', function (err, file) {
-  if (err) throw err;
-  console.log('Saved!');
-});
+// fs.open(OUTPUT_FILE, 'w', function (err, file) {
+//   if (err) throw err;
+//   console.log('Saved!');
+// });

From d8650829fc712d20bfdf5573dcd8f1c11dfbef36 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Tue, 21 Feb 2023 13:41:12 -0500
Subject: [PATCH 09/13] Correct output for combined file

---
 src/cli.js | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/cli.js b/src/cli.js
index ae6d66c..3f3c0f7 100755
--- a/src/cli.js
+++ b/src/cli.js
@@ -32,11 +32,18 @@ export async function search (queryString, options) {
 }
 
 export async function download (startDate, endDate, options) {
-  const source = options.source ?? 'biorxiv';
+  try {
+    const source = options.source ?? 'biorxiv';
 
-  const res = await performDownload(source, startDate, endDate);
+    const res = await performDownload(source, startDate, endDate);
 
-  await sendOutput(res, options);
+    await sendOutput(res, options);
+
+    return res;
+  } catch (err) {
+    console.error(`Error in download: ${err}`);
+    throw err;
+  }
 }
 
 export async function sendOutput (res, options, queryString) {

From 10eabad0dbeb56f02d8c55bb5131ef258d3656ae Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Wed, 22 Feb 2023 12:03:19 -0500
Subject: [PATCH 10/13] Adding keyword search

---
 src/data-search.js | 36 ++++++++++++++++++++----------------
 1 file changed, 20 insertions(+), 16 deletions(-)

diff --git a/src/data-search.js b/src/data-search.js
index 1652042..da2e7e5 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -3,7 +3,7 @@
 // here we will convert the search.sh script into JS
 import { format, sub } from 'date-fns';
 import fs from 'fs';
-import { download, sendOutput } from './cli.js';
+import { download, search, sendOutput } from './cli.js';
 
 const CATEGORY_ID = 'alzheimers-disease';
 const DATA_DIRECTORY = 'example-data';
@@ -27,11 +27,11 @@ fs.open(BIORXIV_FILE, 'w', function (err, file) { // consider changing the callb
   if (err) throw err;
   console.log('Saved!');
 });
-const bioInfo = {
+const bioOptions = {
   source: BIORXIV_SOURCE,
   output: BIORXIV_FILE
 };
-const bioData = await download(START_DATE, END_DATE, bioInfo);
+const bioData = await download(START_DATE, END_DATE, bioOptions);
 
 // Getting all latest articles from MedrXiv
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
@@ -39,11 +39,11 @@ fs.open(MEDRXIV_FILE, 'w', function (err, file) {
   if (err) throw err;
   console.log('Saved!');
 });
-const medInfo = {
+const medOptions = {
   source: MEDRXIV_SOURCE,
   output: MEDRXIV_FILE
 };
-const medData = await download(START_DATE, END_DATE, medInfo);
+const medData = await download(START_DATE, END_DATE, medOptions);
 
 // Creating a JSON with all the results, both sources combined
 console.log('Combining results...');
@@ -55,18 +55,22 @@ const combinedData = {
   ...bioData,
   ...medData
 };
-const combinedInfo = {
+const combinedOptions = {
   output: COMBINED_FILE
 };
-sendOutput(combinedData, combinedInfo);
+sendOutput(combinedData, combinedOptions);
 
 // Search for the QUERY keyword in all the downloaded articles & compile the related articles
-// const QUERY = 'alzheimer';
-// console.log(`Searching for ${QUERY}`);
-// const searchHits = search(QUERY, true); // also unsure about param 2
-// const numSearchHits = Object.keys(searchHits).length;
-// console.log(`Found ${numSearchHits} hits`);
-// fs.open(OUTPUT_FILE, 'w', function (err, file) {
-//   if (err) throw err;
-//   console.log('Saved!');
-// });
+const QUERY = 'alzheimer';
+fs.open(OUTPUT_FILE, 'w', function (err, file) {
+  if (err) throw err;
+  console.log('Saved!');
+});
+const outputOptions = {
+  input: COMBINED_FILE,
+  output: OUTPUT_FILE
+};
+console.log(`Searching for ${QUERY}`);
+const searchHits = await search(QUERY, outputOptions);
+const numSearchHits = Object.keys(searchHits).length;
+console.log(`Found ${numSearchHits} hits`);

From 8240f494ee0559265f95b28be01a98ebbf20409d Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Wed, 22 Feb 2023 13:25:20 -0500
Subject: [PATCH 11/13] Fixed JSON.parse() error

---
 src/data-search.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/data-search.js b/src/data-search.js
index da2e7e5..3ade0ca 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -58,7 +58,7 @@ const combinedData = {
 const combinedOptions = {
   output: COMBINED_FILE
 };
-sendOutput(combinedData, combinedOptions);
+await sendOutput(combinedData, combinedOptions);
 
 // Search for the QUERY keyword in all the downloaded articles & compile the related articles
 const QUERY = 'alzheimer';

From 1e9ea5a6841691f91336b157f9c942f05fe62269 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Wed, 22 Feb 2023 18:01:03 -0500
Subject: [PATCH 12/13] Completed data-search.js

---
 src/cli.js         | 21 ++++++++++++++-------
 src/data-search.js |  7 ++-----
 2 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/src/cli.js b/src/cli.js
index 3f3c0f7..0f66e01 100755
--- a/src/cli.js
+++ b/src/cli.js
@@ -18,17 +18,24 @@ const printText = text => console.log(text);
 const getPrettyText = (articles, queryString, options) => prettyArticles(articles, queryString, options);
 
 export async function search (queryString, options) {
-  const searcher = new Search();
+  try {
+    const searcher = new Search();
+
+    const articles = await getInput(options);
 
-  const articles = await getInput(options);
+    await searcher.articles(articles);
 
-  await searcher.articles(articles);
+    const res = await searcher.search(queryString, {
+      combineWith: options.strict ? 'AND' : 'OR'
+    });
 
-  const res = await searcher.search(queryString, {
-    combineWith: options.strict ? 'AND' : 'OR'
-  });
+    await sendOutput(res, options, queryString);
 
-  await sendOutput(res, options, queryString);
+    return res;
+  } catch (err) {
+    console.error(`Error in search: ${err}`);
+    throw err;
+  }
 }
 
 export async function download (startDate, endDate, options) {
diff --git a/src/data-search.js b/src/data-search.js
index 3ade0ca..af8d687 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -51,10 +51,7 @@ fs.open(COMBINED_FILE, 'w', function (err, file) {
   if (err) throw err;
   console.log('Saved!');
 });
-const combinedData = {
-  ...bioData,
-  ...medData
-};
+const combinedData = bioData.concat(medData);
 const combinedOptions = {
   output: COMBINED_FILE
 };
@@ -72,5 +69,5 @@ const outputOptions = {
 };
 console.log(`Searching for ${QUERY}`);
 const searchHits = await search(QUERY, outputOptions);
-const numSearchHits = Object.keys(searchHits).length;
+const numSearchHits = searchHits.length;
 console.log(`Found ${numSearchHits} hits`);

From 775d08a301566bc43329502936e07c7b9c905092 Mon Sep 17 00:00:00 2001
From: Suhyma <suhyma02@gmail.com>
Date: Fri, 24 Feb 2023 18:15:47 -0500
Subject: [PATCH 13/13] Using promises to open new files

---
 src/data-search.js | 22 +++++-----------------
 1 file changed, 5 insertions(+), 17 deletions(-)

diff --git a/src/data-search.js b/src/data-search.js
index af8d687..eaf4f14 100644
--- a/src/data-search.js
+++ b/src/data-search.js
@@ -2,7 +2,7 @@
 
 // here we will convert the search.sh script into JS
 import { format, sub } from 'date-fns';
-import fs from 'fs';
+import fs from 'fs/promises';
 import { download, search, sendOutput } from './cli.js';
 
 const CATEGORY_ID = 'alzheimers-disease';
@@ -23,10 +23,7 @@ const OUTPUT_FILE = `${DATA_DIRECTORY}/${CATEGORY_ID}.json`;
 
 // Getting all latest articles from BiorXiv
 console.log(`Fetching from ${BIORXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-fs.open(BIORXIV_FILE, 'w', function (err, file) { // consider changing the callback function if needed
-  if (err) throw err;
-  console.log('Saved!');
-});
+fs.open(BIORXIV_FILE, 'w');
 const bioOptions = {
   source: BIORXIV_SOURCE,
   output: BIORXIV_FILE
@@ -35,10 +32,7 @@ const bioData = await download(START_DATE, END_DATE, bioOptions);
 
 // Getting all latest articles from MedrXiv
 console.log(`Fetching from ${MEDRXIV_SOURCE} between ${START_DATE} and ${END_DATE}`);
-fs.open(MEDRXIV_FILE, 'w', function (err, file) {
-  if (err) throw err;
-  console.log('Saved!');
-});
+fs.open(MEDRXIV_FILE, 'w');
 const medOptions = {
   source: MEDRXIV_SOURCE,
   output: MEDRXIV_FILE
@@ -47,10 +41,7 @@ const medData = await download(START_DATE, END_DATE, medOptions);
 
 // Creating a JSON with all the results, both sources combined
 console.log('Combining results...');
-fs.open(COMBINED_FILE, 'w', function (err, file) {
-  if (err) throw err;
-  console.log('Saved!');
-});
+fs.open(COMBINED_FILE, 'w');
 const combinedData = bioData.concat(medData);
 const combinedOptions = {
   output: COMBINED_FILE
@@ -59,10 +50,7 @@ await sendOutput(combinedData, combinedOptions);
 
 // Search for the QUERY keyword in all the downloaded articles & compile the related articles
 const QUERY = 'alzheimer';
-fs.open(OUTPUT_FILE, 'w', function (err, file) {
-  if (err) throw err;
-  console.log('Saved!');
-});
+fs.open(OUTPUT_FILE, 'w');
 const outputOptions = {
   input: COMBINED_FILE,
   output: OUTPUT_FILE